Peifeng Ruan Lab

Welcome to the Dr. Peifeng Ruan Lab!

I am an Assistant Professor at the Quantitative Biomedical Research Center at UT Southwestern Medical Center (UTSW). Before arriving at UTSW, I completed my postdoctoral training in the Department of Biostatistics at Yale University. I received my Ph.D. degree in Biostatistics from The George Washington University and my Ph.D. degree in Computer Science at Fudan University.

Our lab's research interests focus on developing statistical methods and computational algorithms for multi-omics data with applications in complex human diseases, such as heart disease and cancer.

Research Interests

Multi-omics integration

Statistical analysis of network data

High dimensional data analysis

Latest Publications

A complete publication list can be found here.

MORE PUBLICATIONS

Evaluation of a large-scale aptamer proteomics platform among patients with kidney failure on dialysis

Yue Ren, Peifeng Ruan, Mark Segal, Mirela Dobre, Jeffrey R Schelling, Upasana Banerjee, Tariq Shafi, Peter Ganz, Ruth F Dubin, CRIC Study Investigators (2023)
PloS one 18 (12), e0293945

publisher's website

Integrative multi-omics analysis reveals novel idiopathic pulmonary fibrosis endotypes associated with disease progression

Peifeng Ruan, Jamie L Todd, Hongyu Zhao, Yi Liu, Richard Vinisko, Julia F Soellner, Ramona Schmid, Robert J Kaner, Tracy R Luckhardt, Megan L Neely, Imre Noth, Mary Porteous, Rishi Raj, Zeenat Safdar, Mary E Strek, Christian Hesslinger, Scott M Palmer, Thomas B Leonard, Margaret L Salisbury (2023).
Respiratory Research

publisher's website

DiSNEP: a Disease-Specific gene Network Enhancement to improve Prioritizing candidate disease genes

P Ruan, S Wang (2021).
Briefings in Bioinformatics 22 (4), bbaa241

publisher's website

Research Interests

Multi-omics integration

Publications

Ruan, P., Todd, J.L., Zhao, H., Liu, Y., Vinisko, R., Soellner, J.F., Schmid, R., Kaner, R.J., Luckhardt, T.R., Neely, M.L. and Noth, I., 2023. Integrative multi-omics analysis reveals novel idiopathic pulmonary fibrosis endotypes associated with disease progression. Respiratory Research, 24(1), p.141.

Ruan, P., Wang, Y., Shen, R. and Wang, S., 2019. Using association signal annotations to boost similarity network fusion. Bioinformatics, 35(19), pp.3718-3726.

Ren, Y., Ruan, P., Segal, M., Dobre, M., Schelling, J.R., Banerjee, U., Shafi, T., Ganz, P., Dubin, R.F. and CRIC Study Investigators, 2023. Evaluation of a large-scale aptamer proteomics platform among patients with kidney failure on dialysis. PloS one, 18(12), p.e0293945.
Statistical analysis of network data

Publications

Ruan, P. and Wang, S., 2021. DiSNEP: a disease-specific gene network enhancement to improve prioritizing candidate disease genes. Briefings in Bioinformatics, 22(4), p.bbaa241.

Ruan, P., Shen, J., Santella, R.M., Zhou, S. and Wang, S., 2016. NEpiC: a network-assisted algorithm for epigenetic studies using mean and variance combined signals. Nucleic acids research, 44(16), pp.e134-e134.

Wang, Y., Qian, M., Ruan, P., Teschendorff, A.E. and Wang, S., 2019. Detection of epigenetic field defects using a weighted epigenetic distance-based method. Nucleic acids research, 47(1), pp.e6-e6.
High dimensional data analysis

Publications

Ruan, P., Wang, S. and Liang, H., 2020. mirPLS: a partial linear structure identifier method for cancer subtyping using microRNAs. Bioinformatics, 36(19), pp.4902-4909.

Huang, H., Shangguan, J., Ruan, P. and Liang, H., 2019. Bi-level feature selection in high dimensional AFT models with applications to a genomic study. Statistical applications in genetics and molecular biology, 18(5).

Software

DiSNEP

Link

- R package for an improved analytical tool for prioritizing genes associated with diseases using gene network information.
- Reference: Ruan, P. and Wang S. DiSNEP: a Disease-Specific gene Network Enhancement to improve Prioritizing candidate disease genes. Accepted by Briefings in Bioinformatics.
mirPLS

Link

- R package for a partial linear structure identifier algorithm identifying non-linearly outcome-associated miRNAs for cancer subtyping.
- Reference: Ruan, P., Wang, S. and Liang, H. mirPLS: A Partial Linear Structure Identifier Method for Cancer Subtyping Using MicroRNAs. Bioinformatics, btaa606.
abSNF

Link

- R package for an algorithm using association signal annotation to boost similarity network fusion for diseases subtyping.
- Reference: Ruan, P., Wang, Y., Shen, R., and Wang, S. (2019). Using Association Signal Annotations to Boost Similarity Network Fusion.Bioinformatics, 35(19): 3718-3726.
NEpiC

Link

- R package for a biological network assisted greedy algorithm for identifying epigenetic biomarkers.
- Reference: Ruan, P., Shen, J., Santella, R. M., Zhou, S., and Wang, S. (2016) NEpiC: a Network-Assisted Algorithm for Epigenetic Studies Using Mean and Variance Combined Signals. Nucleic Acids Research, 44(16), e134-e134.

Publications

Filter by year:

Evaluation of a large-scale aptamer proteomics platform among patients with kidney failure on dialysis

Yue Ren, Peifeng Ruan, Mark Segal, Mirela Dobre, Jeffrey R Schelling, Upasana Banerjee, Tariq Shafi, Peter Ganz, Ruth F Dubin, CRIC Study Investigators

Dec. 2023PloS one 18 (12), e0293945

Integrative multi-omics analysis reveals novel idiopathic pulmonary fibrosis endotypes associated with disease progression

Dec. 2023Respiratory Research 24 (1), 1-12

DiSNEP: a Disease-Specific gene Network Enhancement to improve Prioritizing candidate disease genes

P Ruan, S Wang

July 2021Briefings in Bioinformatics 22 (4), bbaa241

mirPLS: a partial linear structure identifier method for cancer subtyping using microRNAs

P Ruan, S Wang, H Liang

Oct. 2020Bioinformatics 36 (19), 4902-4909

Advanced Statistical Models in Cancer Research with Omics Data

P Ruan

2020The George Washington University

Detection of Epigenetic Field Defects Using a Weighted Epigenetic Distance-Based Method

Y Wang, M Qian, P Ruan, AE Teschendorff, S Wang

2020Stem Cell Transcriptional Networks, 109-131

Using association signal annotations to boost similarity network fusion

P Ruan, Y Wang, R Shen, S Wang

Oct. 2019Bioinformatics 35 (19), 3718-3726

Bi-level feature selection in high dimensional AFT models with applications to a genomic study

H Huang, J Shangguan, P Ruan, H Liang

Oct. 2019Statistical applications in genetics and molecular biology 18 (5)

Detection of epigenetic field defects using a weighted epigenetic distance-based method

Y Wang, M Qian, P Ruan, AE Teschendorff, S Wang

Jan. 2019Nucleic acids research 47 (1), e6-e6

NEpiC: a network-assisted algorithm for epigenetic studies using mean and variance combined signals

P Ruan, J Shen, RM Santella, S Zhou, S Wang

Sept. 2016BioRxiv, 382549

About PI

Peifeng Ruan

Assistant Professor, Quantitative Biomedical Research Center, UT Southwestern Medical Center

Peifeng.Ruan@UTSouthwestern.edu

5323 Harry Hines Blvd. Dallas, TX 75390

Download CV

Biography

Our lab's research interests focus on developing statistical methods and computational algorithms for multi-omics data with applications in complex human diseases, such as heart disease and cancer.

Positions and Scientific Appointments

present 2022

Assistant Professor
UT Southwestern Medical Center, Dallas, TX
2022 2020

Postdoctoral Associate

Joint program with Boehringer Ingelheim
Yale University, New Haven, CT
2015 2014

Visiting Scholar
Columbia University Medical Center, New York, NY

Education

2020 2016

Ph.D. in Biostatistics
The George Washington University, Washington, DC
2015 2010

Ph.D. in Computer Science
Fudan University, Shanghai, China
2012 2011

M.A. in Statistics
Columbia University, New York, NY
2010 2006

B.S. in Applied Mathematics
Fudan University, Shanghai, China

Peifeng Ruan Lab

Research Interests

Latest Publications

Evaluation of a large-scale aptamer proteomics platform among patients with kidney failure on dialysis

Integrative multi-omics analysis reveals novel idiopathic pulmonary fibrosis endotypes associated with disease progression

DiSNEP: a Disease-Specific gene Network Enhancement to improve Prioritizing candidate disease genes

Research Interests

Multi-omics integration

Statistical analysis of network data

High dimensional data analysis

Software

DiSNEP

mirPLS

abSNF

NEpiC

Publications

Members

Bo Yao

Peiran Quan

Ismael Villanueva-Miranda

About PI

Peifeng Ruan

Biography

Positions and Scientific Appointments

Education